This course will provide an introduction to the technology, data analysis, tools and resources used in RNA sequencing and transcriptomics. The content is intended to provide a broad overview of the subject area, and to introduce participants to simple data analysis using  the command line and APIs. It will also highlight key resources, approaches and methodologies to begin the biological interpretation and analysis of transcriptomics data. Topics will be delivered using a mixture of lectures, practical sessions and open discussions. Practical work during the course will use small, example data-sets - there will be no opportunity to  analyse personal data.

Who is this course for?

This course is aimed at life science researchers needing to learn more about the basic processing of raw RNA-Seq data and downstream analysis. It will help those wanting to learn how to interpret gene expression data and explore results of biological significance from processed data.

Participants will require a basic knowledge of the Unix command line, the Ubuntu 18 operating system and the R statistical packages. We recommend these free tutorials:

• Basic introduction to the Unix environment: www.ee.surrey.ac.uk/Teaching/Unix
• Introduction and exercises for Linux: https://training.linuxfoundation.org/free-linux-training
• Basic R concept tutorials: www.r-tutor.com/r-introduction

Regardless of your current knowledge we encourage successful participants to use these, and other materials, to prepare for attending the course and future work in this area.

What will I learn?

Learning outcomes

After this course you should be able to:

• Describe a variety of applications and workflow approaches for NGS technologies
• Use a range of bioinformatics software and tools to undertake basic analysis of RNA-Seq data
• Evaluate the advantages and limitations of NGS analyses
• Interpret and annotate data with functional information using public resources

Course content

During this course you will learn about:

• NGS platforms and NGS data files and formats
• RNA-Seq bioinformatics workflow steps following sequence generation
• NGS for transcriptomics; QC, mapping, visualisation tools
• Data resources to assist in the functional analysis and interpretation of biological data
• Data resources covered:
  • ArrayExpress and Expression Atlas
  • European Nucleotide Archive
  • Reactome
  • Open Targets

Trainers

Please read our page on application advice before starting your application. In order to be considered for a place on this course, you must do the following:

1. Complete the online application form
2. Submit a Microsoft Word (.docx) document containing three short paragraphs with a biography, work history and description of your current research interests; each paragraph should be no more than 100 words
3. Provide a letter of support from a supervisor or a senior co-worker explaining why you should be selected for this course

Please submit all documents to Johanna Langrish (johanna@ebi.ac.uk) by 12:00 GMT on Friday 11 January, 2019.

Incomplete applications will not be considered.

Accommodation will be provided at the Holiday Inn, Impington Tuesday-Friday inclusive. This location is difficult to access from both the Wellcome Genome Campus or Cambridge and we strongly recommend that successful participants consider finding alternative accommodation close to Cambridge Station prior to or after the course to ease journeys. Please contact the Wellcome Genome Campus Conference Centre directly if you wish to arrange to stay additional nights around the course dates.

The course includes evening meals at the Hinxton Hall Restaurant on campus or the Red Lion Pub in nearby Hinxton village, and breaks and lunches outside the EMBL-EBI training rooms.